Tandem mass spectrometry is widely used for trace analysis and for the determination of the structures of ions. In tandem mass spectrometry a first mass analyzer selects ions of one particular mass to charge ratio (or range of mass to charge ratios) from ions supplied by an ion source, the ions are fragmented and a second mass analyzer records the mass spectrum of the fragment ions. In a triple quadrupole mass spectrometer system, this effects MS/MS. Ions produced in an atmospheric pressure source, pass through a region of dry nitrogen and then pass through a small orifice, into a region at a pressure of several torr. The ions then pass through a quadrupole ion guide, operated a pressure of about 7.times.10-3 torr into a first quadrupole mass analyzer, operated at a pressure of about 2.times.10-5 torr. Precursor ions mass selected in the first quadrupole mass analyzer are injected into a collision cell filled with an inert gas, such as argon, of a pressure of 10.sup.-4 to 10.sup.-2 torr. The collision cell contains a second quadrupole (or multipole) ion guide, to confine ions to the axis. Ions gain internal energy through collisions with gas and then fragment the fragment ions and any undissociated precursor ions then pass into a third quadrupole, which forms a second mass analyzer, and then to a detector, where the mass spectrum is recorded.
Triple quadrupole systems are widely used for tandem mass spectrometry. One limitation is that recording a fragment mass spectrum can be time consuming because the second mass analyzer must step through many masses to record a complete spectrum. As in any scanning mass analyzer, all other ions (outside of `transmission window`) are lost for analysis, thus reducing the duty cycle to values of around 0.1% or less. To overcome these limitations, QqTOF systems have been developed (as described for example in: Morris, H. R.; Pacton, T; Dell, A.; Langhorne, J.; Berg. M.; Bordoli, R. S.; Hoyes, J.; Bateman, R. H.; Rapid Commun. Mass Spectrometry, 1996, 10, 889-896; and Shevchenko, A.; Chernushevich, I.; Ens, W.; Standing, K. G.; Thomson, B.; Wilm, M.; Mann, M., Rapid Commun. Mass Spectrometry, 1997, 11, 1015-1024). This system is similar to the triple quadrupole system but the second mass analyzer is replaced by a time-of-flight mass analyzer, TOF. The advantage of the TOF is that it can record 10.sup.4 or more complete mass spectra in one second without scanning. Thus for applications where a complete mass spectrum of fragment ions is desired the duty cycle is greatly improved with a TOF mass analyzer and spectra can be acquired more quickly. Alternatively for a given measurement time, spectra can be acquired on a smaller amount of sample.
A further known technique is the coupling of electrospray ionization (ESI) to time-of-flight mass spectrometers (TOFMS), and this is an attractive technique for mass spectrometry. ESI is a soft ionization technique capable of forming ions from a broad range of biomolecules, while TOFMS has the well known advantages of rapid mass scanning, high sensitivity, and a theoretically limitless mass range. However, ESI and TOFMS are, in one way, incompatible as a source/analyzer pair: ESI creates a continuous stream of ions and TOFMS requires pulsed operation. Thus in the simplest coupling of ESI to TOFMS there is a very poor duty cycle, with less than 1% of the ions formed being detected (to obtain reasonable mass resolution) and early work in this field was predominantly concerned with increasing the duty cycle.
Within the past two years, literature on ESI-TOFMS has begun to focus on tandem mass spectrometry (MS/MS) with hybrid instruments. The fragmentation of ions in these systems is achieved via traditional methods for collision induced dissociation (CID). Tandem-in-space systems termed quadrupole-TOF's (QqTOF or QTOF), as noted above, are analogous to triple quadrupole mass spectrometers--the precursor ion is selected in a quadrupole mass filter, dissociated in a radiofrequency- (RF-) only multipole collision cell, and the resultant fragments are analyzed in a TOFMS. Tandem-in-time systems use a 3-D ion trap mass spectrometer (ITMS) for selecting and fragmenting the precursor ion, but pulse the fragment ions out of the trap and into a TOFMS for mass analysis.
Tandem mass spectrometers (in particular, triple quadrupoles and QqTOFs) are often used to perform a technique known as a parent ion scan (or precursor ion scan). In this technique, the first mass resolving quadrupole is scanned in order to sequentially transmit parent ions over a selected mass range. The second mass spectrometer is used to selectively transmit only one specific fragment or product ion from the collision cell. The mass spectrum thus produced by scanning the first mass spectrometer shows only those ions from the ion source which fragment to produce the specific product ion. Thus from a complex mixture of ionized species, a simple mass spectrum showing only those components which produce the known fragment ion is produced. This method is often used in order to identify parent ions as candidates for full MS/MS. For example, if the sample contains a mixture of many different species, and the only compounds of interest are those which have a structure known to always generate a fragment of m/z 86, then a parent ion scan may be performed in order to identify which parent ions form m/z 86. A full MS/MS spectrum may then be performed on those few parent ions, instead of on every peak in the Q1 mass spectrum. In this way, a significant amount of time can be saved in analyzing the sample.
In triple quadrupoles, parent ion scans have proved to be the right tool to search for ions of certain classes of compounds, e.g. peptides.sup.1, glycopeptides.sup.2 or phosphopeptides.sup.3 (as detailed, for example in the following references for these three classes of compounds: .sup.1 M. Wilm, G. Neubauer and M. Mann, Anal. Chem., 1996, 68, pp. 527-533; .sup.2 S. A. Carr, M. J. Huddleston and M. F. Bean, Protein Science, 1993, 2, pp. 183-196; .sup.3 S. A. Carr, M. J. Huddleston and R. S. Annan, Anal. Biochem., 1996, 239, pp. 180-192). However, a current limitation of the Qq-TOFs is their lower sensitivity in this particular mode of operation, compared to triple quadrupoles. The last mass analyzer (TOF or Q3) does not need to scan in this mode, and the Qq-TOF does not benefit from simultaneous ion detection in TOF. On the other hand, more ions are lost in a TOF compared to a third quadrupole: at the entrance, on grids, and mostly due to duty cycle.
The problem here is that usually the fragment ions cover a large m/z range, and the TOF instrument has to capture all that m/z range if consecutive spectra are not to overlap. If one is interested in just a particular mass, then this can lead to a low duty cycle.
There are two main factors governing the duty cycle of an orthogonal acceleration TOF instrument when operated in the conventional (continuous beam) mode. Generally, you have to wait for the heaviest ions to reach the detector before the next pulse of ions can be introduced. Since the width of the entrance window is only a fraction of the transverse distance between the ion storage region and the detector, even the heaviest ions will overfill this region before the next pulse of ions can be released. The loss due to this effect is simply equal to the ratio of the length of the entrance window to the distance between the storage region and the detector. This ratio is often 1:4, giving a maximum duty cycle of 25% (achievable only for the heaviest ions).
Additionally, there is a loss factor due to the mass-dependent velocities of the ions. This is due to the fact that ions have a constant transverse energy, which means that the velocities of the lighter ions are higher than those of heavier ions (in the ratio of the square root of the ratio of the masses). This means that the duty cycle loss of lighter ions is larger than that of the heaviest ions in the spectrum, that is the lighter ions tend to overfill the ion storage region to an even greater extent than the heavier ions. For example, if ions of up to m/z 2000 are present, and one is particularly interested only in m/z 200, then the additional loss factor is: ##EQU1##
Putting together the loss factor for the heaviest ions, plus the additional loss factor for lighter ions, gives for m/z 200 a total duty cycle of approximately 31.6% time 25%, which is approximately equal to 8%.
It has been known to provide ion traps in a TOF mass spectrometer (although not in a QqTOF type of arrangement, using the collision cell as the ion trap). Thus, U.S. Pat. No. 5,689,111 (Dresch et al and assigned to Analytica of Brantford) describes an instrument which provides a linear two-dimensional ion guide with a time of flight mass analyzer. The ion guide is a multipole ion guide. However, while the intention is to improve the duty cycle, a single ion guide is provided extending through two different chambers. An ion entrance section of the ion guide is located in a region where background gas pressure is in the viscous flow regime and the pressure along the ion guide drops to molecular flow pressure regimes at the ion exit section. The ion guide is switched to operate as an ion trap. However, this is not a tandem instrument in that there is only a single multipole ion guide. Thus, this instrument can only detect ions in a certain mass range, and does not have the ability to provide an upstream mass resolving section to select ions of interest. There is no recognition that this method can be applied to enhance the sensitivity of an MS/MS device where ions are coming out of a collision cell. Nor is there any indication that it can be used to enhance sensitivity in any situation where one or more specific ions (fragments or precursors) are desired to be monitored. Specifically, there is no indication that the method can be used to enhance the sensitivity in a parent ion scan mode, MRM mode, or neutral loss scan mode.
Another proposal is found in U.S. Pat. No. 5,763,878. This discloses a method and device for orthogonal injection into a time of flight mass spectrometer. It provides a somewhat unusual arrangement in which the multipole rod set extends through to the time of flight instrument. Ions are then pulsed out from one of the rod sets into the field free drift region of the time of flight instrument. However, again, there is no provision of an upstream mass resolving section. Also, both these patents do not discuss or mention a parent ion scanning technique, and do not mention any MS/MS scanning methods.